Installing GreyFace's patch allows window mode to be run on modern systems, I get that.

But trying to use any of the other res tools to set a different resolution, I can then never enter window mode again with the .exes they create, it always tells me I must be at 16 bit color. From all the posts I've read it seems like people are able to set their resolution and still play in window. How can I do this? Nothing is working.

I haven't tried any of the higher resolution packs so this may not help but you tried the resolution pack listed on the website where you download the grayface patch right? If not it may just be the one you are using is incompatible with grayface.